Thanks for the quick reply.
I'm attaching the the picture how it looks like. But when the issue occurs, it doesn't matter which script. It's happening for all scripts.
Find attached the pictures and find below the aclient.log of one of the servers which has the issue:
[12/28/2011 17:05:38.126 4560 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 02:05:6.262 4560 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 02:05:6.730 4560 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 02:08:29.474 3200 0] bootstrap.cpp:1125 - Error reading input file.
[12/29/2011 02:13:7.185 3200 0] bootstrap.cpp:461 GetCfgFilename(): strName = C:
[12/29/2011 02:13:8.259 3964 0] ReplyUpdateComputer.cpp:190 - Error removing registry value.
[12/29/2011 02:13:8.259 3964 0] ReplyUpdateComputer.cpp:296 - Error reading logevent status from registry.
[12/29/2011 02:13:12.091 3232 0] DsAgent.cpp:744 CDSAgent::InvokeHandler() - Caught ... Exception.
[12/29/2011 02:27:4.291 3316 0] bootstrap.cpp:1125 - Error reading input file.
[12/29/2011 02:31:39.497 3316 0] bootstrap.cpp:461 GetCfgFilename(): strName = C:
[12/29/2011 02:31:41.120 6132 0] ReplyUpdateComputer.cpp:190 - Error removing registry value.
[12/29/2011 02:31:41.120 6132 0] ReplyUpdateComputer.cpp:296 - Error reading logevent status from registry.
[12/29/2011 02:31:46.634 1116 0] DsAgent.cpp:744 CDSAgent::InvokeHandler() - Caught ... Exception.
[12/29/2011 10:34:13.362 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 12:14:6.168 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 14:47:0.088 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 16:07:42.071 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 16:22:4.086 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 17:10:17.310 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 17:12:5.188 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 17:19:38.978 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 18:47:2.634 988 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/29/2011 22:01:18.701 27436 0] main.cpp:724 - Toolbox List is empty, exiting
[12/29/2011 22:01:53.801 14752 0] main.cpp:724 - Toolbox List is empty, exiting
[12/30/2011 00:08:39.501 16356 0] bootstrap.cpp:1125 - Error reading input file.
[12/30/2011 00:08:39.798 16356 0] bootstrap.cpp:461 GetCfgFilename(): strName = C:
[12/30/2011 00:08:42.902 7948 0] ReplyUpdateComputer.cpp:190 - Error removing registry value.
[12/30/2011 00:08:42.902 7948 0] ReplyUpdateComputer.cpp:296 - Error reading logevent status from registry.
[12/30/2011 00:08:47.507 2348 0] DsAgent.cpp:744 CDSAgent::InvokeHandler() - Caught ... Exception.
[12/30/2011 00:31:15.387 14056 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/30/2011 02:16:4.846 14056 0] UiPipeListenerThread.cpp:77 - CUiPipeListener::Run caught CIPCError exception, removing UI from List.
[12/30/2011 02:19:37.376 3296 0] bootstrap.cpp:1125 - Error reading input file.
[12/30/2011 02:25:40.046 3296 0] bootstrap.cpp:461 GetCfgFilename(): strName = C:
[12/30/2011 02:25:46.429 5816 0] ReplyUpdateComputer.cpp:190 - Error removing registry value.
[12/30/2011 02:25:46.429 5816 0] ReplyUpdateComputer.cpp:296 - Error reading logevent status from registry.
[12/30/2011 02:25:51.041 6680 0] DsAgent.cpp:744 CDSAgent::InvokeHandler() - Caught ... Exception.
And, currently only affecting our latest deployment on Windows 2008 R2 SP1 deployments.